Contacts of the strand formed by residues 299 - 307 (chain B) in PDB entry 3I8E
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B LEU* 4.2 5.4 - - - +
248B ILE* 4.7 5.7 - - - +
285B LEU* 3.9 0.2 - - - -
286B GLU* 2.8 46.6 + - + +
297B LEU* 3.7 2.2 - - - +
298B LYS* 1.3 88.8 - - + +
300B LEU* 1.3 87.7 + - - +
301B ARG* 5.2 3.6 - - - +
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ILE* 5.3 2.2 - - + -
237B ILE* 4.4 15.3 - - + -
238B THR 4.6 9.9 - - - +
239B TYR* 4.6 7.0 - - + -
246B LEU* 3.5 41.7 - - + -
247B ALA 4.5 2.2 - - - +
248B ILE* 3.6 41.1 - - + +
283B LEU* 4.7 6.3 - - + -
284B LEU 3.2 15.5 - - - +
285B LEU* 3.5 26.0 - - + -
297B LEU* 6.1 0.2 - - + -
299B ASP* 1.3 93.6 + - - +
301B ARG* 1.3 65.3 + - - +
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Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ILE* 3.9 10.9 - - + +
282B MET 3.6 1.0 - - - +
283B LEU* 4.2 1.2 - - - +
284B LEU* 3.1 66.0 + - - +
286B GLU* 4.2 19.4 + - - +
299B ASP* 5.2 4.0 - - - +
300B LEU* 1.3 78.1 - - - +
302B VAL* 1.3 86.5 + - - +
303B GLU* 4.2 18.7 + - - +
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ILE* 3.6 29.4 - - + -
248B ILE* 4.0 7.4 - - + -
250B PRO* 4.5 11.7 - - + +
252B ILE* 4.5 12.7 - - + +
253B ILE* 4.0 20.0 - - + -
273B LEU* 4.6 4.0 - - + -
281B PHE* 3.7 23.3 - - + -
282B MET 3.6 6.7 - - - +
283B LEU* 3.9 13.0 - - + -
301B ARG* 1.3 90.8 - - - +
303B GLU* 1.3 72.2 + - - +
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ILE* 6.1 0.4 - - - -
281B PHE* 3.5 10.3 - - - -
282B MET* 3.2 40.8 + - + +
284B LEU* 4.4 13.4 - - + +
301B ARG* 4.2 20.8 + - - +
302B VAL* 1.3 76.3 - - - +
304B LEU* 1.3 62.2 + - - +
305B LEU* 3.9 4.9 - - + +
346B TYR* 4.3 25.8 + - - -
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ILE* 3.6 31.6 - - + +
279B ARG* 4.2 22.9 - - + +
280B LEU 4.1 2.5 - - - +
281B PHE* 3.7 26.0 - - + -
303B GLU* 1.3 75.2 + - - +
305B LEU* 1.3 60.5 + - - +
306B GLY* 3.5 29.2 - - - +
344B GLY 4.5 4.2 - - - +
346B TYR* 3.9 15.3 - - - -
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU* 3.8 14.8 - - + -
280B LEU* 2.9 22.1 + - + +
281B PHE 4.2 1.1 - - - +
282B MET* 3.5 47.6 - - + -
303B GLU* 3.9 5.7 - - + +
304B LEU* 1.3 72.4 - - - +
306B GLY* 1.3 57.4 + - - +
336B LEU* 3.8 24.7 - - + -
337B ASN 5.4 1.1 - - - +
344B GLY 5.0 0.4 - - - -
345B SER* 3.8 0.9 - - - -
346B TYR* 2.9 56.7 + - + -
347B VAL* 3.1 17.4 + - + -
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Residues in contact with GLY 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B ARG* 3.5 7.8 - - - +
280B LEU 3.2 21.6 + - - -
304B LEU* 3.4 16.7 - - - +
305B LEU* 1.3 82.3 - - - +
307B GLU* 1.3 60.6 + - - +
344B GLY 5.3 1.1 - - - -
345B SER* 3.6 13.9 - - - -
347B VAL* 3.9 5.8 - - - +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B GLU 4.6 2.8 - - - +
278B GLY* 4.5 4.4 - - - -
279B ARG* 4.5 8.6 - - + +
306B GLY* 1.3 73.7 - - - +
308B THR* 1.3 72.1 + - - +
332B GLN* 5.0 0.2 + - - -
334B VAL* 5.6 0.2 - - - +
345B SER* 4.2 5.8 + - - +
347B VAL* 3.6 13.8 - - - +
383B LYS* 3.5 34.4 + - - +
753B ARG* 4.4 10.6 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il